Details

    • Type: Improvement Improvement
    • Status: Closed Closed
    • Priority: Minor Minor
    • Resolution: Implemented
    • Affects Version/s: None
    • Fix Version/s: 1.7.1
    • Component/s: None
    • Labels:
      None

      Description

      The location of sub-workflows is recorded as an absolute path. This can cause problems when a hierarchy of workflows is moved aroound a file system or between machines.

        Issue Links

          Activity

          June Finch (Inactive) made changes -
          Field Original Value New Value
          Fix Version/s T2 guideline [ 10038 ]
          Assignee June Finch [ jfinch ] Tom Oinn [ toinn ]
          Stian Soiland-Reyes made changes -
          Assignee Tom Oinn [ toinn ] Alan Williams [ awilliams ]
          Fix Version/s 1.7.1 [ 10054 ]
          Fix Version/s T2 guideline [ 10038 ]
          Priority Major [ 3 ] Critical [ 2 ]
          Alan Williams made changes -
          Assignee Alan Williams [ awilliams ] David Withers [ witherd5 ]
          Hide
          Stian Soiland-Reyes added a comment -

          My suggestions:

          The easiest way to work around this bug without handcrafting the XML is to in Taverna where the workflow containing a nested workflow has been correctly loaded, right click on the nested workflow and select "Edit nested workflow". Click the "Workflows" menu and go back to the parent workflow. This should have created a copy of the nested workflow so that if you now save the parent, the nested workflow will be saved as part of the SCUFL of the parent.

          We'll try to find a way to improve this, one reason why some users still like the reference version is that they can then update the nested workflow, save it, and all of the workflows including that as a nested workflow would use the new version.

          My suggestion for how we (the developers) are going to fixing this is to show this explicitly in the GUI and not just in the XML, and allow the user to choose which one they want to go for, the copy or the filename, and additionally to save the filename as a relative reference if possible.

          myExperiment should also give a warning if people try to upload a workflow with such missing references.

          Another workaround is to use "Add Nested Workflow ... Open Location" and paste in the download URL of the nested workflow as it is on myExperiment. As long as the other user of the parent workflow is connected to the Internet, myExperiment is online, and the other user has access to the nested workflow there, such a parent workflow would also be shareable.

          Show
          Stian Soiland-Reyes added a comment - My suggestions: The easiest way to work around this bug without handcrafting the XML is to in Taverna where the workflow containing a nested workflow has been correctly loaded, right click on the nested workflow and select "Edit nested workflow". Click the "Workflows" menu and go back to the parent workflow. This should have created a copy of the nested workflow so that if you now save the parent, the nested workflow will be saved as part of the SCUFL of the parent. We'll try to find a way to improve this, one reason why some users still like the reference version is that they can then update the nested workflow, save it, and all of the workflows including that as a nested workflow would use the new version. My suggestion for how we (the developers) are going to fixing this is to show this explicitly in the GUI and not just in the XML, and allow the user to choose which one they want to go for, the copy or the filename, and additionally to save the filename as a relative reference if possible. myExperiment should also give a warning if people try to upload a workflow with such missing references. Another workaround is to use "Add Nested Workflow ... Open Location" and paste in the download URL of the nested workflow as it is on myExperiment. As long as the other user of the parent workflow is connected to the Internet, myExperiment is online, and the other user has access to the nested workflow there, such a parent workflow would also be shareable.
          Stian Soiland-Reyes made changes -
          Link This issue depends on TAV-559 [ TAV-559 ]
          David Withers (Inactive) made changes -
          Assignee David Withers [ witherd5 ] Ian Dunlop [ ian ]
          Ian Dunlop made changes -
          Status Open [ 1 ] Prioritised [ 10000 ]
          Priority Critical [ 2 ] Minor [ 4 ]
          Ian Dunlop made changes -
          Status Prioritised [ 10000 ] Analysis In Progress [ 10004 ]
          Analysis If the URL of a WorkflowProcessor is null then it writes out the full XML for the processor, otherwise it puts a link to the file instead.
          Hide
          Ian Dunlop added a comment -

          Setting the URL temporarily to null in a nested workflow forces it to be written out in full when saving the SCUFL

          Show
          Ian Dunlop added a comment - Setting the URL temporarily to null in a nested workflow forces it to be written out in full when saving the SCUFL
          Ian Dunlop made changes -
          Status Analysis In Progress [ 10004 ] Analysed [ 10001 ]
          Assignee Ian Dunlop [ ian ] Alan Williams [ awilliams ]
          Ian Dunlop made changes -
          Assignee Alan Williams [ awilliams ] Ian Dunlop [ ian ]
          Ian Dunlop made changes -
          Status Analysed [ 10001 ] Planned [ 10002 ]
          Ian Dunlop made changes -
          Status Planned [ 10002 ] Implementation In Progress [ 10005 ]
          Hide
          Ian Dunlop added a comment -

          In the SaveWorkflowAction it uses a new JFileChooser called NestedFileChooser which has a checkbox to select saving the full nested workflow or not. If you check this box ithe SaveWorkflowAction uses a NestedWorkflowSwitch which can set the nested workflow to null. This causes it to write it's XML out in full. The same class is then used to reset the URL back to what it was later.

          Show
          Ian Dunlop added a comment - In the SaveWorkflowAction it uses a new JFileChooser called NestedFileChooser which has a checkbox to select saving the full nested workflow or not. If you check this box ithe SaveWorkflowAction uses a NestedWorkflowSwitch which can set the nested workflow to null. This causes it to write it's XML out in full. The same class is then used to reset the URL back to what it was later.
          Ian Dunlop made changes -
          Status Implementation In Progress [ 10005 ] Closed [ 6 ]
          Resolution Implemented [ 11 ]
          David Withers (Inactive) made changes -
          Workflow New features and improvements [ 10888 ] jira [ 11900 ]
          Alan Williams made changes -
          Component/s Taverna Enactor [ 10003 ]

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            People

            • Assignee:
              Ian Dunlop
              Reporter:
              Alan Williams
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              Dates

              • Created:
                Updated:
                Resolved: